Background: An overlap of systemic lupus erythematosus (SLE) and antineutrophil cytoplasmic antibodies-(ANCA-) associated vasculitis (AAV) is extremely uncommon and no clear definition has been proposed. The SLE/AAV overlap syndrome mainly affects kidney, blood count, nervous system and lung. However, few previous cases reported nasal septal and palatal perforation in this disorder. Case Presentation: We presented a case of a 16-year-old female with a 6-month history of SLE, developed perforation of the nasal septum and palate. She was diagnosed with SLE due to facial malar rash, oral ulcer, increased erythrocyte sedimentation rate (ESR), low complement levels, and positive anti-Smith antibody. Approximately 6 months later, she had a perforation of the nasal septum and palate with positive anti-proteinase 3 antibody (anti-PR3-ANCA). A nasal endoscopic biopsy revealed an inflammatory polyp with chronic suppurative inflammation and inflammatory granulomatous hyperplasia. In this case, the clinical, biological, radiological, and histological findings substantiated the diagnosis of AAV. Infections, drug abuse, malignancies, IgG4-related disease (IgG4-RD) and trauma were excluded. So we diagnosed her with SLE/AAV overlap syndrome.Conclusion: When a patient's symptoms cannot be explained by one disease, we need to consider the overlapping of two diseases, especially in patients with autoimmune diseases.